I am preparing a manuscript in LaTeX. The journal (Physical Biology, an IOP publication) requires that figures be saved in .eps format, so I am trying to do that. However, I cannot get my LaTeX file to build when I have generated the .eps files on my Ubuntu computer. If I save the images on my Mac, the file build just fine.

So far, I have tried saving images in ImageJ, FIJI and Inkscape. The same problem occurs in all three. When using kile, I get the following error:

1 Answer
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According to section 2.16 of the TexShop documentation ("Shell escape protection"), the shell escape feature is to allow pdflatex to run other programs during compilation. In particular, the epstopdf package you are using to convert eps to pdf is such a program (incidentally, you don't have to explicitly turn that on anymore in the latest versions of TeXLive).

I am not familiar with kile or TeXWorks, but I expect they have an option in the preferences that let's you turn on the shell escape, just as in TeXShop. You can also explicitly compile your LaTeX file from the command line: pdflatex --shell-escape file.tex where file.tex is the name of your file.

It sounds like the reason you can typeset your file on the Mac but not Ubuntu, is either: 1) Your Mac version(s) of your TeX apps have shell escape enabled, or 2) When you make your eps file on the Mac, it additionally creates pdf versions, which are later found by your TeX app and so no conversion from eps is needed.